Shewanella oncorhynchi sp. nov., a novel member of the genus Shewanella, isolated from Rainbow Trout (Oncorhynchus mykiss)

Altun, Soner; Duman, Muhammed; Ay, Hilal; Satıcıoğlu, İzzet Burçin

doi:10.1099/ijsem.0.005460

Cited by 15 publications

(15 citation statements)

References 46 publications

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“…Contrary to previous studies by Castillo et al (2018a) and Topić Popović et al (2022), S. baltica was not detected in freshwater fish in our study. Interestingly, a high number of diverse strains isolated in our study belonged to the recently described S. oncorhynchi (Altun et al, 2022). Our S. oncorhynchi strains were highly similar (97.0%–97.8%) to the unclassified strain Shewanella sp.…”

Section: Discussionmentioning

confidence: 64%

“…S. glacialipiscicola and S. oncorhynchi showed the lowest G + C content of 44.1% and 45.2%–45.5%, respectively, which differs from S. xiamenensis , S. oneidensis , S. baltica and S. hafniensis . The variances in G + C content between strains of the same species were ≤0.5% and showed high similarity to the appropriate reference strains (Altun et al, 2022; Huang et al, 2010; Martín‐Rodríguez & Meier‐Kolthoff, 2022).…”

Section: Discussionmentioning

confidence: 83%

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Phylogenetic analysis of Shewanella spp. isolated from fish

Paździor,

Bomba,

Tłuścik

et al. 2023

Journal of Fish Diseases

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Different species of Shewanella spp. widely inhabit freshwater and marine environments. Some of them are opportunistic fish pathogens. The application of high‐throughput sequencing enabled the characterization and taxonomic reclassification of many Shewanella spp. species. Still, some strains collected from fish need to be better recognized. The aim of the present study was to classify and determine the phylogenetic relationships of Shewanella spp. collected from fish. The complete genomes of 94 strains of Shewanella spp. from different fish species were sequenced using Illumina platform (MiSeq). The 16S rRNA gene, genomic features and whole‐genome relationships of those bacteria were comprehensively analysed in comparison to reference strains. Whole‐genome analysis showed that the tested Shewanella spp. strains were clustered into six groups similar to reference strains of S. xiamenensis, S. oneidensis, S. glacialipiscicola, S. hafniensis, S. baltica and S. oncorhynchi. Our study indicates that the whole‐genome sequence analysis enabled taxonomic classification and assessment of the diversity of the Shewanella spp. strains, as opposed to recently the gold standard method of 16S rRNA amplicon sequencing. The high genetic diversity and low similarity to the reference genome of S. oneidensis indicate that the group of strains may be a subspecies or even new species. Furthermore, we showed that the most frequent Shewanella spp. species occurring in freshwater fish in our study is the recently described species S. oncorhynchi.

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Section: Discussionmentioning

confidence: 64%

Section: Discussionmentioning

confidence: 83%

Phylogenetic analysis of Shewanella spp. isolated from fish

Paździor,

Bomba,

Tłuścik

et al. 2023

Journal of Fish Diseases

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“…Until now, the genus Shewanella comprised 82 validly published species [3], inhabiting various environments, e.g. marine sediments, freshwater, iron-rich sediment, and fish [4–8]. Shewanella has been shown to utilize diverse electron acceptors in anaerobic respiration of various energy sources, such as nitrate, nitrite, thiosulphate and iron oxide.…”

Section: Introductionmentioning

confidence: 99%

Isolation and genomics of ten novel Shewanella species from mangrove wetland

Liu

Yang

Rao

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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Mangrove bacteria largely compose the microbial community of the coastal ecosystem and are directly associated with nutrient cycling. In the present study, 12 Gram-negative and motile strains were isolated from a mangrove wetland in Zhangzhou, China. Pairwise comparisons (based on 16S rRNA gene sequences) and phylogenetic analysis indicated that these 12 strains belong to the genus Shewanella . The 16S rRNA gene sequence similarities among the 12 Shewanella strains and their related type strains ranged from 98.8 to 99.8 %, but they still could not be considered as known species. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the 12 strains and their related type strains were below the cut-off values (ANI 95–96% and dDDH 70 %) for prokaryotic species delineation. The DNA G+C contents of the present study strains ranged from 44.4 to 53.8 %. The predominant menaquinone present in all strains was MK-7. The present study strains (except FJAT-53532T) also contained ubiquinones (Q-8 and Q-7). The polar lipid phosphatidylglycerol and fatty acid iso-C15 : 0 was noticed in all strains. Based on phenotypic, chemotaxonomic, phylogenetic and genomic comparisons, we propose that these 12 strains represent 10 novel species within the genus Shewanella , with the names Shewanella psychrotolerans sp. nov. (FJAT-53749T=GDMCC 1.2398T=KCTC 82649T), Shewanella zhangzhouensis sp. nov. (FJAT-52072T=MCCC 1K05363T=KCTC 82447T), Shewanella rhizosphaerae sp. nov. (FJAT-53764T=GDMCC 1.2349T=KCTC 82648T), Shewanella mesophila sp. nov. (FJAT-53870T=GDMCC 1.2346T= KCTC 82640T), Shewanella halotolerans sp. nov. (FJAT-53555T=GDMCC 1.2344T=KCTC 82645T), Shewanella aegiceratis sp. nov. (FJAT-53532T=GDMCC 1.2343T=KCTC 82644T), Shewanella alkalitolerans sp. nov. (FJAT-54031T=GDMCC 1.2347T=KCTC 82642T), Shewanella spartinae sp. nov. (FJAT-53681T=GDMCC 1.2345T=KCTC 82641T), Shewanella acanthi sp. nov. (FJAT-51860T=GDMCC 1.2342T=KCTC 82650T) and Shewanella mangrovisoli sp. nov. (FJAT-51754T=GDMCC 1.2341T= KCTC 82647T).

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“…Finally, our analysis did not identify bacterial strains harboring more than one T3SS2 gene cluster within their genomes. Interestingly, several of these T3SS2 were identified in recently isolated and/or classified Vibrio and Shewanella species, including V. paracholerae [74], V. tarriae [75], V. tetraodonis [76], S. oncorhynchi [77] and S. psychropiezotolerans [78] ( Fig. 2 and Table S1 ).…”

Section: Resultsmentioning

confidence: 99%

TheVibrioType III Secretion System 2 is not restricted to theVibrionaceaeand encodes differentially distributed repertoires of effector proteins

Jerez

Plaza

Bravo

et al. 2022

Preprint

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Vibrio parahaemolyticus is the leading cause of seafood-borne gastroenteritis worldwide. A distinctive feature of the O3:K6 pandemic clone, and its derivatives, is the presence of a second, phylogenetically distinct, Type III Secretion System (T3SS2) encoded within the genomic island VPaI-7. The T3SS2 allows the delivery of effector proteins directly into the cytosol of infected eukaryotic cells to subvert key host cell processes, critical for V. parahaemolyticus to colonize and cause disease. Furthermore, the T3SS2 also increases the environmental fitness of V. parahaemolyticus in its interaction with bacterivorous protists; hence it has been proposed that it contributed to the global oceanic spread of the pandemic clone. Several reports have identified T3SS2-related genes in Vibrio and non-Vibrio species, suggesting that the T3SS2 gene cluster is not restricted to the Vibrionaceae and can mobilize through horizontal gene transfer events. In this work, we performed a large-scale genomic analysis to determine the phylogenetic distribution of the T3SS2 gene cluster and its repertoire of effector proteins. We identified putative T3SS2 gene clusters in 1130 bacterial genomes from eight bacterial genera and five bacterial families. A hierarchical clustering analysis allowed us to define six T3SS2 subgroups (I-VI) with different repertoires of T3SS2 effector proteins, redefining the concepts of T3SS2 core and accessory effector proteins. Finally, we identified a subset of T3SS2 gene clusters that lack most T3SS2 effector proteins described to date and provided a list of 10 novel effector candidates for this subgroup through bioinformatic analysis. Collectively, our findings indicate that the T3SS2 extends beyond the Vibrionaceae family and suggest that different effector protein repertories could have a differential impact on the pathogenic potential and environmental fitness of all the bacteria that have acquired the Vibrio T3SS2 gene cluster.

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Shewanella oncorhynchi sp. nov., a novel member of the genus Shewanella, isolated from Rainbow Trout (Oncorhynchus mykiss)

Cited by 15 publications

References 46 publications

Phylogenetic analysis of Shewanella spp. isolated from fish

Phylogenetic analysis of Shewanella spp. isolated from fish

Isolation and genomics of ten novel Shewanella species from mangrove wetland

TheVibrioType III Secretion System 2 is not restricted to theVibrionaceaeand encodes differentially distributed repertoires of effector proteins

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